I bought some neodymium magnets a long time ago... they are 6.5mm square by 2.5mm in height. Since you have the 3D model, you can adjust for this however you like.

I also canibalized a couple USB cables for the female/male connectors... and the male/female barrel bits of an old dead walwart. Alternatively, you could use the male USB part from DigiKey pictured.

An exacto knife, ham sandwich, and three magic beans might also be helpful but not required.

The fastest path to completion for a build will be to print the base and bottom of the berry first. Then, end with the body of the berry. Whilst the berry body cranketh away, you can get the fiber optic in place, place the barrel connectors, slap the USB connectors on, solder like a monkey, and adjust how the Rasberry Pi fits.

One design consideration was how to work-around the massive SD card. I have an adapter that I used to reduce the height of the body. If you make the berry case and send me a picture of it - I'll send you an adapter for free.

If you're interested in setting up your very berry dock as a laptop as pictured - you should checkout the amazing tutorial at Adafruit. There are a couple special cables and an HDMI adapter you'll need.

Good point... I just added a note to the body - the model is assembled for display. You'll need to divide it into printable chunks. There's a lot going on inside the berry - zoom-in and you'll see what I mean.